Re: [Bioc-devel] Request to Retire COHCAP Bioconductor Package
Hi Lori, Thank you very much for your help. As long as it won't be a problem that I don't think my COH e-mail address will not be able to receive messages after 4/30, then I agree to direct removal. I believe this is what has been discussed with Yate-Ching and Xiwei, in terms of the general topic. If I understand correctly, then I appreciate you helping skip a release in the depreciation state (prior to removal). Thank you again! Sincerely, Charles From: Kern, Lori Sent: Tuesday, April 16, 2024 3:56 AM To: bioc-devel@r-project.org ; Charles Warden Cc: Xiwei Wu ; Yate-Ching Yuan Subject: Re: Request to Retire COHCAP Bioconductor Package We normally like to do a full round of a package in a deprecation state before removal completely (so deprecated in Bioc 3. 19 and removed in Bioc 3. 20) but since there are no reverse dependencies, I don't think this should be an issue to directly We normally like to do a full round of a package in a deprecation state before removal completely (so deprecated in Bioc 3.19 and removed in Bioc 3.20) but since there are no reverse dependencies, I don't think this should be an issue to directly remove from 3.19 without deprecation. Please confirm direct removal over standard deprecation processes and I can take care of this. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Charles Warden via Bioc-devel Sent: Monday, April 15, 2024 7:14 PM To: bioc-devel@r-project.org Cc: Xiwei Wu ; Yate-Ching Yuan Subject: [Bioc-devel] Request to Retire COHCAP Bioconductor Package Hi, I have greatly appreciated the assistance provided by Bioconductor support over several years! However, my requested end date to work in the Integrative Genomics Core at City of Hope is 4/30/2024. Later this year, I will be starting a PhD program at UC-Riverside. When I was previously in graduate school at the University of Michigan, I switched to using my personal e-mail address to support the COHCAP Bioconductor package. However, we would prefer to improve the transition this time that I am going to graduate school. So, after a number of discussions, we have decided to request to retire the COHCAP Bioconductor package (https://secure-web.cisco.com/18MW32Nmr7CBKJg3Ep7wXuI8t3lFqrL7diwmsQYI7dBiV2DnODHyT7MEKyQI_XbTm9SxFc-X59sAg_eJO5wjVcXo1_bK66HNtSdjt5vNojTo5hKNWi-Dl8DW2oDONNXjUjpvl9NTJOO3l5YjYsbzM3Nl2bQvljjnk3VZeY1qwvpf7cG1BJhQHY3RL7WpoFTiBYyCxK8HqpNz1dhxGBJOTBFDm0w-8leXCP7NCojJat40_hGb6YIofwnhi39okN_Clxzp0gzb8FQRap2AT3oyNiEZKelvaNxWXUmh2abcTYFawXskGOEAWZXfQv5BTmpkp/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FCOHCAP.html<https://urldefense.com/v3/__https://secure-web.cisco.com/18MW32Nmr7CBKJg3Ep7wXuI8t3lFqrL7diwmsQYI7dBiV2DnODHyT7MEKyQI_XbTm9SxFc-X59sAg_eJO5wjVcXo1_bK66HNtSdjt5vNojTo5hKNWi-Dl8DW2oDONNXjUjpvl9NTJOO3l5YjYsbzM3Nl2bQvljjnk3VZeY1qwvpf7cG1BJhQHY3RL7WpoFTiBYyCxK8HqpNz1dhxGBJOTBFDm0w-8leXCP7NCojJat40_hGb6YIofwnhi39okN_Clxzp0gzb8FQRap2AT3oyNiEZKelvaNxWXUmh2abcTYFawXskGOEAWZXfQv5BTmpkp/https*3A*2F*2Fwww.bioconductor.org*2Fpackages*2Frelease*2Fbioc*2Fhtml*2FCOHCAP.html__;JSUlJSUlJSU!!Fou38LsQmgU!uWc7ww_XZfnKhhJUiq7VW2aYtjdigWtUnfXNLYtseToHYuSyJTDxUZBq8jHfBYg13v06txiJvX-WHSgyDkU5zL0JVA$>). We will instead request users to go to the source page on GitHub (https://secure-web.cisco.com/1j9Obf_O7HxIn__GrQM5CQS_vyKFobzQGg5-jot9RzFCjkUGpO1HaL4J4Adtt605Oq38PACHleEPSjAb5snp2drWgmWmB6FxuGzqlL9OWz2QFJxu1TKALIhHYujdQJS-2mP2a9XdUEB-_sp4ipEwnETlWLuOI9ExJulZ2LNOQ-fC7N1ZUTo29RGbD-fFRI-MXYemgl_nph8dRYz_1TOTLiIBSPeCu42J362tgxREQM3YrbFIkkjD88aM5CGs9UWNI7xNKWB2JucADbBq1n8bu9sec4G5raWiZ4r2zSF4quP3JtCRG8OpUgu_KBca9hWSQ61AXx0yfOKhXzb7mhejUog/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP<https://urldefense.com/v3/__https://secure-web.cisco.com/1j9Obf_O7HxIn__GrQM5CQS_vyKFobzQGg5-jot9RzFCjkUGpO1HaL4J4Adtt605Oq38PACHleEPSjAb5snp2drWgmWmB6FxuGzqlL9OWz2QFJxu1TKALIhHYujdQJS-2mP2a9XdUEB-_sp4ipEwnETlWLuOI9ExJulZ2LNOQ-fC7N1ZUTo29RGbD-fFRI-MXYemgl_nph8dRYz_1TOTLiIBSPeCu42J362tgxREQM3YrbFIkkjD88aM5CGs9UWNI7xNKWB2JucADbBq1n8bu9sec4G5raWiZ4r2zSF4quP3JtCRG8OpUgu_KBca9hWSQ61AXx0yfOKhXzb7mhejUog/https*3A*2F*2Fgithub.com*2Fcwarden45*2FCOHCAP__;JSUlJSU!!Fou38LsQmgU!uWc7ww_XZfnKhhJUiq7VW2aYtjdigWtUnfXNLYtseToHYuSyJTDxUZBq8jHfBYg13v06txiJvX-WHSgyDkWLf_x_mA$>), where we have made changes in the README file. I have cc'd Yate-Ching Yuan (the Bioinformatics Director, at the time of development of the original code) as well as Xiwei Wu (the Integrative Genomics Core Director, where I currently work and where I was working when the code was first converted to be provided through Bioconductor). Since we won't be making changes for future formatting requirements and we don't want to use a non-COH e-mail address as a support con
[Bioc-devel] Request to Retire COHCAP Bioconductor Package
Hi, I have greatly appreciated the assistance provided by Bioconductor support over several years! However, my requested end date to work in the Integrative Genomics Core at City of Hope is 4/30/2024. Later this year, I will be starting a PhD program at UC-Riverside. When I was previously in graduate school at the University of Michigan, I switched to using my personal e-mail address to support the COHCAP Bioconductor package. However, we would prefer to improve the transition this time that I am going to graduate school. So, after a number of discussions, we have decided to request to retire the COHCAP Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html). We will instead request users to go to the source page on GitHub (https://github.com/cwarden45/COHCAP), where we have made changes in the README file. I have cc'd Yate-Ching Yuan (the Bioinformatics Director, at the time of development of the original code) as well as Xiwei Wu (the Integrative Genomics Core Director, where I currently work and where I was working when the code was first converted to be provided through Bioconductor). Since we won't be making changes for future formatting requirements and we don't want to use a non-COH e-mail address as a support contact, can you please help with actively removing the COHCAP package from Bioconductor (before 4/30)? Thank you very much! Sincerely, Charles Charles Warden, Bioinformatics Specialist (He/Him) Integrative Genomics Core Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA 91016) Room 1086 Internal Ext: 80375 | Direct: (626) 218-0375 -- -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to rec eive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
Hi Everybody,
It looks like the error is now fixed (from changing the Perl code) in the
release and devel versions:
https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html
https://www.bioconductor.org/packages/devel/bioc/html/COHCAP.html
I noticed there wasn't a Mac test for the devel version, but perhaps that is
true for all packages?
Thank you very much for your help!
Sincerely,
Charles
-Original Message-
From: Hervé Pagès
Sent: Tuesday, April 28, 2020 10:55 AM
To: Charles Warden ; Shepherd, Lori
; 'bioc-devel@r-project.org'
Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
It is not clear what the purpose of these "if" statement is. Apparently to set
the $os_name variable but then where is this variable used and for what?
So you might want to revisit the need for these tests. Maybe you don't need
them after all.
Another problem is that the temporary files generated by your Perl scripts are
generated in the current working directory. As discussed earlier, this is not
good. Please make sure that all temporary files are generated in tempdir().
Thanks!
H.
On 4/28/20 10:43, Charles Warden wrote:
> Hi H,
>
> Thank you for pointing that out.
>
> I am currently not seeing errors on my Windows computer, but I see that I
> need to add "msys" for Windows on your system (and add quotes as well as make
> the error message more clear). I have a 64-bit Windows computer and I didn't
> get an error message, but I can see how this could cause problems. I
> apologize for not realizing that.
>
> It sounds like I should wait a little while to do that. However, I think
> this does sound correct, and I will make that change.
>
> Thank You,
> Charles
>
> -Original Message-----
> From: Hervé Pagès
> Sent: Tuesday, April 28, 2020 10:32 AM
> To: Charles Warden ; Shepherd, Lori
> ; 'bioc-devel@r-project.org'
>
> Subject: Re: [Bioc-devel] Windows Development Build Error Message for
> COHCAP
>
> Hi Charles,
>
> The error you get on Windows is because your Perl script integrate_island.pl
> fails on this platform. It contains the following code:
>
> if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
> {
> #Mac
> $os_name = "MAC";
> }#end if ($os eq "MacOS")
> elsif ($os eq "MSWin32")
> {
> #PC
> $os_name = "PC";
> }#end if ($os eq "MacOS")
> else
> {
> print "Need to specify folder structure for $os!\n";
> exit;
> }#end else
>
> The major problem with this code is that the script will exit
> **normally** without doing anything if the detected OS is not one of the
> expected ones. So the 'temp_paired_367853.txt' file is not produced and your
> R code later fails to open it (when you try to read the file with
> read.table()).
>
> Note that before exiting, your Perl script displays:
>
> Need to specify folder structure for msys!
>
> which you can see in the report. This gives you a BIG clue of what the
> problem is and how to fix it.
>
> If you develop your package on Windows (and it seems you do), the
> problem should be very reproducible for you, granted that you use R
> 4.0.0 for that of course.
>
> Thanks,
> H.
>
>
> On 4/28/20 09:02, Charles Warden wrote:
>> Hi Lori,
>>
>> Thank you very much.
>>
>> I was thinking about reverting the change to test not specifying the
>> full file path at one point (in *v1.33.6*), but I was planning on
>> keeping the change to using a temporary directory in *v1.33.4*.
>> Essentially, I tested making that change in *v1.33.6* because there
>> was still an error message in *v1.33.4.*
>>
>> However, I will wait to see what else you suggest, before making any
>> additional changes. From my end, there is no need to rush, and I can
>> wait until next week (or later).
>>
>> You probably already know this, but it looks like *v1.33.6 *is in the
>> release version without any errors (although it does look like the
>> Windows version is different):
>>
>> https://urldefense.com/v3/__https://www.bioconductor.org/packages/rel
>> e
>> ase/bioc/html/COHCAP.html__;!!Fou38LsQmgU!_wdP4PPRbzvocGetxQ4gXCipwd4
>> _
>> 1cOH4l3X1xkG8DChTNm0z7KryGwjVxBW$
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconducto
>> r
>> .org_packages_release_bioc_html_COHCAP.html=DwMGaQ=eRAMFD45gAfqt8
>> 4
>> VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJ
Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
Hi H,
Thank you for pointing that out.
I am currently not seeing errors on my Windows computer, but I see that I need
to add "msys" for Windows on your system (and add quotes as well as make the
error message more clear). I have a 64-bit Windows computer and I didn't get
an error message, but I can see how this could cause problems. I apologize for
not realizing that.
It sounds like I should wait a little while to do that. However, I think this
does sound correct, and I will make that change.
Thank You,
Charles
-Original Message-
From: Hervé Pagès
Sent: Tuesday, April 28, 2020 10:32 AM
To: Charles Warden ; Shepherd, Lori
; 'bioc-devel@r-project.org'
Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
Hi Charles,
The error you get on Windows is because your Perl script integrate_island.pl
fails on this platform. It contains the following code:
if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
{
#Mac
$os_name = "MAC";
}#end if ($os eq "MacOS")
elsif ($os eq "MSWin32")
{
#PC
$os_name = "PC";
}#end if ($os eq "MacOS")
else
{
print "Need to specify folder structure for $os!\n";
exit;
}#end else
The major problem with this code is that the script will exit
**normally** without doing anything if the detected OS is not one of the
expected ones. So the 'temp_paired_367853.txt' file is not produced and your R
code later fails to open it (when you try to read the file with read.table()).
Note that before exiting, your Perl script displays:
Need to specify folder structure for msys!
which you can see in the report. This gives you a BIG clue of what the problem
is and how to fix it.
If you develop your package on Windows (and it seems you do), the problem
should be very reproducible for you, granted that you use R
4.0.0 for that of course.
Thanks,
H.
On 4/28/20 09:02, Charles Warden wrote:
> Hi Lori,
>
> Thank you very much.
>
> I was thinking about reverting the change to test not specifying the
> full file path at one point (in *v1.33.6*), but I was planning on
> keeping the change to using a temporary directory in *v1.33.4*.
> Essentially, I tested making that change in *v1.33.6* because there
> was still an error message in *v1.33.4.*
>
> However, I will wait to see what else you suggest, before making any
> additional changes. From my end, there is no need to rush, and I can
> wait until next week (or later).
>
> You probably already know this, but it looks like *v1.33.6 *is in the
> release version without any errors (although it does look like the
> Windows version is different):
>
> https://urldefense.com/v3/__https://www.bioconductor.org/packages/rele
> ase/bioc/html/COHCAP.html__;!!Fou38LsQmgU!_wdP4PPRbzvocGetxQ4gXCipwd4_
> 1cOH4l3X1xkG8DChTNm0z7KryGwjVxBW$
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor
> .org_packages_release_bioc_html_COHCAP.html=DwMGaQ=eRAMFD45gAfqt84
> VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=OANP0q_4ipib1q
> 0Y0KadeY9Api_-E4mZFZDodVQ8gMY=9TOVgc79RcLRStlZDJLBYL-wmdRF4rBN6aWrEG
> gHdGQ=>
>
> So, if I understand everything, I think this is OK.
>
> Thanks Again,
>
> Charles
>
> *From:*Shepherd, Lori
> *Sent:* Tuesday, April 28, 2020 5:29 AM
> *To:* Charles Warden ; Hervé Pagès
> ; 'bioc-devel@r-project.org'
>
> *Subject:* Re: [Bioc-devel] Windows Development Build Error Message
> for COHCAP
>
> I can investigate more on the windows machine after we are done with
> the release (later this week -- possibly early next)
>
> I would highly recommend not reverting the change to using a
> temporary directory. We don't normally allow anyone to write to
> anywhere but a temporary directory except in extreme circumstances.
> New packages that are reviewed would not get accepted in Bioconductor if they
> did this.
>
> We appreciate your effort on trying to debug this and will help you
> shortly.
>
> Cheers,
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> --
> --
>
> *From:*Charles Warden mailto:cwar...@coh.org>>
> *Sent:* Monday, April 27, 2020 12:27 PM
> *To:* Hervé Pagès <mailto:hpa...@fredhutch.org>>; Shepherd, Lori
> mailto:lori.sheph...@roswellpark.org>>;
> 'bioc-devel@r-project.org'
> mailto:bioc-devel@r-project
Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
Hi Lori,
Thank you very much.
I was thinking about reverting the change to test not specifying the full file
path at one point (in v1.33.6), but I was planning on keeping the change to
using a temporary directory in v1.33.4. Essentially, I tested making that
change in v1.33.6 because there was still an error message in v1.33.4.
However, I will wait to see what else you suggest, before making any additional
changes. From my end, there is no need to rush, and I can wait until next week
(or later).
You probably already know this, but it looks like v1.33.6 is in the release
version without any errors (although it does look like the Windows version is
different):
https://www.bioconductor.org/packages/release/bioc/html/COHCAP.html
So, if I understand everything, I think this is OK.
Thanks Again,
Charles
From: Shepherd, Lori
Sent: Tuesday, April 28, 2020 5:29 AM
To: Charles Warden ; Hervé Pagès ;
'bioc-devel@r-project.org'
Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
I can investigate more on the windows machine after we are done with the
release (later this week -- possibly early next)
I would highly recommend not reverting the change to using a temporary
directory. We don't normally allow anyone to write to anywhere but a temporary
directory except in extreme circumstances. New packages that are reviewed
would not get accepted in Bioconductor if they did this.
We appreciate your effort on trying to debug this and will help you shortly.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
____
From: Charles Warden mailto:cwar...@coh.org>>
Sent: Monday, April 27, 2020 12:27 PM
To: Hervé Pagès mailto:hpa...@fredhutch.org>>; Shepherd,
Lori mailto:lori.sheph...@roswellpark.org>>;
'bioc-devel@r-project.org'
mailto:bioc-devel@r-project.org>>
Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP
Hi,
I am not sure if I am going to have to wait to submit extra revisions.
However, I am unfortunately having the same issue (even though I tested using
the temporary directory instead of the current working directory, in COHCAP
(v.1.33.4).
I also tested changing the file path to the temporary in v.1.33.6, but that
also didn't fix the problem (and I might change that back).
I am also still not able to reproduce this error message on my end.
For example, this is what the output of the build command looks like:
C:\Users\Charles\Documents>"C:\Program Files\R\R-4.0.0\bin\R.exe" CMD build
COHCAP
* checking for file 'COHCAP/DESCRIPTION' ... OK
* preparing 'COHCAP':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'COHCAP_1.33.6.tar.gz'
And, I can also install COHCAP successfully using devtools (in R-4.0.0),
although it does have some warnings:
> library("devtools")
Loading required package: usethis
> devtools::install_github("cwarden45/COHCAP")
Skipping install of 'COHCAP' from a github remote, the SHA1 (09b017ba) has not
changed since last install.
Use `force = TRUE` to force installation
> devtools::install_github("cwarden45/COHCAP", force=TRUE)
Downloading GitHub repo cwarden45/COHCAP@master
checking for file
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
...
checking for file
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
...
√ checking for file
'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
(339ms)
- preparing 'COHCAP':
checking DESCRIPTION meta-information ...
checking DESCRIPTION meta-information ...
√ checking DESCRIPTION meta-information
- cleaning src
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'COHCAP_1.33.6.tar.gz'
Installing package into ‘C:/Users/Charles/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'COHCAP' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include"
-DNDEBUG -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
-I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include'-O2 -Wall
-mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.0/include"
-DNDEBUG -I'C:/Users/Charles/Docume
Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
cessary parentheses in declaration of 'assert_not_arg' [-Wparentheses] failed (boost::mpl::not_:: ^ C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o COHCAP.dll tmp.def RcppExports.o Rcpp_BH_ANOVA.o Rcpp_BH_linear_regression.o Rcpp_BH_ttest.o -LC:/PROGRA~1/R/R-40~1.0/bin/x64 -lR installing to C:/Users/Charles/Documents/R/win-library/4.0/00LOCK-COHCAP/00new/COHCAP/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'COHCAP' finding HTML links ... done COHCAP.BSSeq.preprocess html COHCAP.BSSeq_V2.methyl.tablehtml COHCAP.annotate html COHCAP.avg.by.islandhtml COHCAP.avg.by.site html COHCAP.denovo html COHCAP.integrate.avg.by.island html COHCAP.integrate.avg.by.sitehtml COHCAP.qc html COHCAP.reformatFinalReport html COHCAP.site html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COHCAP) The downloaded source packages are in ‘C:\Users\Charles\AppData\Local\Temp\Rtmp88lsk0\downloaded_packages’ Installation path not writeable, unable to update packages: boot, class, foreign, KernSmooth, MASS, nnet, spatial I am not sure if this last warning about the installation path has something to do with using both the pre-release (previously) and release (currently) versions of R-4.0.0. Can you please help me know if you have any other troubleshooting suggestions for the Window server used to test the Bioconductor packages? Thank You, Charles -Original Message- From: Hervé Pagès Sent: Thursday, April 23, 2020 12:23 PM To: Charles Warden ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP [Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.] -- Hi Charles, On 4/23/20 10:19, Charles Warden wrote: > My guess was that creating the temporary file in the working directory > instead of another folder might help. FWIW here are 2 important reasons for writing temporary stuff to tempdir() instead of the current working directory: 1. tempdir() is the only place that is guaranteed to be writable on every system. Yes the user home is very likely to be writable too but there is actually no guarantee and some systems have unconventional setups where it's not. 2. Whatever you put in tempdir() will automatically be removed at the end of the R session. Even though there are ways to achieve this with the temporary stuff you write in the user home, it's not automatic and hard to get right. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
Hi H, Thank you for the additional information. I have pushed the git updates using tempdir() instead of getwd(). It sounds like that will probably fix the problem, and I will check tomorrow. Best Wishes, Charles -Original Message- From: Hervé Pagès Sent: Thursday, April 23, 2020 12:23 PM To: Charles Warden ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP [Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.] -- Hi Charles, On 4/23/20 10:19, Charles Warden wrote: > My guess was that creating the temporary file in the working directory > instead of another folder might help. FWIW here are 2 important reasons for writing temporary stuff to tempdir() instead of the current working directory: 1. tempdir() is the only place that is guaranteed to be writable on every system. Yes the user home is very likely to be writable too but there is actually no guarantee and some systems have unconventional setups where it's not. 2. Whatever you put in tempdir() will automatically be removed at the end of the R session. Even though there are ways to achieve this with the temporary stuff you write in the user home, it's not automatic and hard to get right. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Windows Development Build Error Message for COHCAP
Hi, I noticed that I received a few error messages in the Windows build for COHCAP: http://bioconductor.org/checkResults/devel/bioc-LATEST/COHCAP/tokay2-buildsrc.html I changed the default settings to avoid an earlier error message (again, just on Windows), but I am currently getting an error message that I am having some trouble reproducing. Can you help me with either of the following questions? 1. I apologize for the simple question, but where can I download the Windows executable for R-4.0.0? I was able to reproduce and fix an earlier issue with R-devel (on Linux), but I was not certain how to get the error message for Windows. I have tried to reproduce the error using the devtools installation from the GitHub code (https://github.com/cwarden45/COHCAP), but that can be installed successfully (with Windows R-3.6.3). 2. The .zip file for the Windows version on the devel page is different (http://bioconductor.org/packages/3.11/bioc/html/COHCAP.html), where I see cohcap_1.33.1.zip for Windows. I think I saw the first error message in 1.33.1, and I made an intermediate change before changing the defaults to avoid the error message. However, the strange thing was that I thought I saw an "OK" status while I was waiting for the 1.33.3 version to appear in the build reports (which I thought was for COHCAP 1.33.2). Do all of the packages get re-built, regardless of whether an update is uploaded? * I am wondering if there is a chance that I might be able to wait a day or two and see if I can get a status of "OK" for all steps on all of the test servers. However, if that is true, then I am a little worried about what happens if there is a temporary error in the release version. Thank you very much! Sincerely, Charles Charles Warden, Bioinformatics Specialist Integrative Genomics Core City of Hope National Medical Center Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016) Room 1086 Internal Ext: 80375 | Direct: 626-218-0375 -- -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to rec eive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Lori,
Thank you very much for your help!
Sincerely,
Charles
From: Shepherd, Lori
Sent: Tuesday, March 24, 2020 5:39 AM
To: Charles Warden ; 'Martin Morgan'
; 'Alexey Sergushichev'
Cc: 'bioc-devel@r-project.org'
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Thank you for your contributions to Bioconductor. We appreciate you fixing
COHCAP.
I will begin the deprecation process for sRAP; there is no further action
needed.
Cheers,
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel
mailto:bioc-devel-boun...@r-project.org>> on
behalf of Charles Warden mailto:cwar...@coh.org>>
Sent: Monday, March 23, 2020 3:53 PM
To: 'Martin Morgan' mailto:mtmorgan.b...@gmail.com>>;
'Alexey Sergushichev' mailto:alserg...@gmail.com>>
Cc: 'bioc-devel@r-project.org'
mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Everybody,
Thank you again for your help!
I think the issue for the COHCAP devel package has now been resolved:
http://bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/<https://urldefense.com/v3/__http:/bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/__;!!Fou38LsQmgU!4pixzueuEashd7OMaAtrxWF6J7-9ZdkNh7lA1938iAeeYvzmbMVMrX-o7Sq7$>
I had somewhat similar error messages for sRAP (which is different than
COHCAP), but I am OK with sRAP being removed from the next version of
Bioconductor (since it is no longer being maintained). If you can please let
me know if there is a contact that I should e-mail (beyond this mailing list,
or not fixing the error), then I would appreciate that.
Thanks Again,
Charles
-----Original Message-
From: Charles Warden
Sent: Friday, March 20, 2020 1:40 PM
To: Martin Morgan mailto:mtmorgan.b...@gmail.com>>;
Alexey Sergushichev mailto:alserg...@gmail.com>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: RE: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Martin,
That is probably what happened.
Thank you again for your help!
Sincerely,
Charles
-Original Message-
From: Martin Morgan mailto:mtmorgan.b...@gmail.com>>
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden mailto:cwar...@coh.org>>; Alexey
Sergushichev mailto:alserg...@gmail.com>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar,
'1.33. 1' ? This generates an error
** using staged installation
Error : Invalid DESCRIPTION file
Malformed package version.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ERROR: installing package DESCRIPTION failed for package ...
Martin
On 3/20/20, 4:28 PM, "Charles Warden"
mailto:cwar...@coh.org>> wrote:
Hi Martin,
I am currently having difficulty reproducing my earlier error (which I
think didn’t even get to the step of testing the demo code). So, I think the
short answer is that I should just use version 1.33.1.
In my search history, I can tell that I Googled "R Malformed package
version," so I think that was part of the earlier message that I got.
For what is worth, I think this is what gave me the idea to change the
version numbering system:
https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$<https://urldefense.com/v3/__https:/cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$>
However, if I am not currently getting an error message, then I won't worry
about it.
Thank you very much for your help!
Sincerely,
Charles
-Original Message-----
From: Martin Morgan
mailto:mtmorgan.b...@gmail.com>>
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden mailto:cwar...@coh.org>>; Alexey
Sergushichev mailto:alserg...@gmail.com>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Can you be precise about the concern about 1.33.1 as a version number (what
precise note / error / warning you received)? This scheme is very standard for
package versions, and as you see enforced (for many years!) by Bioconductor.
Martin
On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden"
mailto:bioc-devel-boun...@r-project.org%20on%20behalf%20of%20cwar...@coh.org>>
wrote:
Hi
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Everybody,
Thank you again for your help!
I think the issue for the COHCAP devel package has now been resolved:
http://bioconductor.org/checkResults/release/bioc-LATEST/COHCAP/
I had somewhat similar error messages for sRAP (which is different than
COHCAP), but I am OK with sRAP being removed from the next version of
Bioconductor (since it is no longer being maintained). If you can please let
me know if there is a contact that I should e-mail (beyond this mailing list,
or not fixing the error), then I would appreciate that.
Thanks Again,
Charles
-Original Message-
From: Charles Warden
Sent: Friday, March 20, 2020 1:40 PM
To: Martin Morgan ; Alexey Sergushichev
Cc: bioc-devel@r-project.org
Subject: RE: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Martin,
That is probably what happened.
Thank you again for your help!
Sincerely,
Charles
-Original Message-
From: Martin Morgan
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden ; Alexey Sergushichev
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar,
'1.33. 1' ? This generates an error
** using staged installation
Error : Invalid DESCRIPTION file
Malformed package version.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ERROR: installing package DESCRIPTION failed for package ...
Martin
On 3/20/20, 4:28 PM, "Charles Warden" wrote:
Hi Martin,
I am currently having difficulty reproducing my earlier error (which I
think didn’t even get to the step of testing the demo code). So, I think the
short answer is that I should just use version 1.33.1.
In my search history, I can tell that I Googled "R Malformed package
version," so I think that was part of the earlier message that I got.
For what is worth, I think this is what gave me the idea to change the
version numbering system:
https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$
However, if I am not currently getting an error message, then I won't worry
about it.
Thank you very much for your help!
Sincerely,
Charles
-Original Message-
From: Martin Morgan
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Can you be precise about the concern about 1.33.1 as a version number (what
precise note / error / warning you received)? This scheme is very standard for
package versions, and as you see enforced (for many years!) by Bioconductor.
Martin
On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden"
wrote:
Hi Everybody,
I think changing that read.table() parameter fixed the main issue.
However, when I tested my code, R used a different way to note versions
in R-v.4.0.0.
For example, in order to clear a message from “R CMD check” or “R CMD
build”, I had to say the version was 1.33-1 (instead of 1.33.1).
I uploaded those changes to GitHub and tested an R-3.6 installation,
and that was OK.
However, when I am working on merging the GitHub and Bioconductor
branches, I get the following error message:
“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“
Is this going to be changed in Bioconductor, or should I see if this is
only a NOTE or WARNING (and submit the package as version 1.33.1)?
Thank You,
Charles
From: Alexey Sergushichev
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden
Cc: Shepherd, Lori ;
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error
Message
I think one of the major changes recently is setting stringsAsFactors
option to FALSE by default.
Best,
Alexey
On Fri, Mar 20, 2020 at 12:48 AM Charles Warden
mailto:cwar...@coh.org>> wrote:
Hi Lori,
Thank you very much.
If I use R-4.0 (instead of R-3.6), then I can reproduce the error
message.
I will work in figuring out why the code works with R-3.6 but not
R-4.0, but it seems like this might affect other packages as well (since I
received error messages for 2 out of 2 of the Bioconductor packages that I
contributed to).
Do you have any general suggestions of what types of new errors might
be encountered from using R-4.0?
Thanks Again,
Charles
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Martin,
That is probably what happened.
Thank you again for your help!
Sincerely,
Charles
-Original Message-
From: Martin Morgan
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden ; Alexey Sergushichev
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar,
'1.33. 1' ? This generates an error
** using staged installation
Error : Invalid DESCRIPTION file
Malformed package version.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ERROR: installing package DESCRIPTION failed for package ...
Martin
On 3/20/20, 4:28 PM, "Charles Warden" wrote:
Hi Martin,
I am currently having difficulty reproducing my earlier error (which I
think didn’t even get to the step of testing the demo code). So, I think the
short answer is that I should just use version 1.33.1.
In my search history, I can tell that I Googled "R Malformed package
version," so I think that was part of the earlier message that I got.
For what is worth, I think this is what gave me the idea to change the
version numbering system:
https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$
However, if I am not currently getting an error message, then I won't worry
about it.
Thank you very much for your help!
Sincerely,
Charles
-Original Message-
From: Martin Morgan
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Can you be precise about the concern about 1.33.1 as a version number (what
precise note / error / warning you received)? This scheme is very standard for
package versions, and as you see enforced (for many years!) by Bioconductor.
Martin
On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden"
wrote:
Hi Everybody,
I think changing that read.table() parameter fixed the main issue.
However, when I tested my code, R used a different way to note versions
in R-v.4.0.0.
For example, in order to clear a message from “R CMD check” or “R CMD
build”, I had to say the version was 1.33-1 (instead of 1.33.1).
I uploaded those changes to GitHub and tested an R-3.6 installation,
and that was OK.
However, when I am working on merging the GitHub and Bioconductor
branches, I get the following error message:
“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“
Is this going to be changed in Bioconductor, or should I see if this is
only a NOTE or WARNING (and submit the package as version 1.33.1)?
Thank You,
Charles
From: Alexey Sergushichev
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden
Cc: Shepherd, Lori ;
bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error
Message
I think one of the major changes recently is setting stringsAsFactors
option to FALSE by default.
Best,
Alexey
On Fri, Mar 20, 2020 at 12:48 AM Charles Warden
mailto:cwar...@coh.org>> wrote:
Hi Lori,
Thank you very much.
If I use R-4.0 (instead of R-3.6), then I can reproduce the error
message.
I will work in figuring out why the code works with R-3.6 but not
R-4.0, but it seems like this might affect other packages as well (since I
received error messages for 2 out of 2 of the Bioconductor packages that I
contributed to).
Do you have any general suggestions of what types of new errors might
be encountered from using R-4.0?
Thanks Again,
Charles
From: Shepherd, Lori
[mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>; Charles
Warden mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message
Yes that is the correct version of R to use. Thank you for taking the
time to make sure everything is correct to debug. We appreciate your effort and
contributors to bioconductor.
Get Outlook for
Android<https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$>
____
From: Charles Warden
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Martin,
I am currently having difficulty reproducing my earlier error (which I think
didn’t even get to the step of testing the demo code). So, I think the short
answer is that I should just use version 1.33.1.
In my search history, I can tell that I Googled "R Malformed package version,"
so I think that was part of the earlier message that I got.
For what is worth, I think this is what gave me the idea to change the version
numbering system:
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file
However, if I am not currently getting an error message, then I won't worry
about it.
Thank you very much for your help!
Sincerely,
Charles
-Original Message-
From: Martin Morgan
Sent: Friday, March 20, 2020 1:09 PM
To: Charles Warden ; Alexey Sergushichev
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Can you be precise about the concern about 1.33.1 as a version number (what
precise note / error / warning you received)? This scheme is very standard for
package versions, and as you see enforced (for many years!) by Bioconductor.
Martin
On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden"
wrote:
Hi Everybody,
I think changing that read.table() parameter fixed the main issue.
However, when I tested my code, R used a different way to note versions in
R-v.4.0.0.
For example, in order to clear a message from “R CMD check” or “R CMD
build”, I had to say the version was 1.33-1 (instead of 1.33.1).
I uploaded those changes to GitHub and tested an R-3.6 installation, and
that was OK.
However, when I am working on merging the GitHub and Bioconductor branches,
I get the following error message:
“Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“
Is this going to be changed in Bioconductor, or should I see if this is
only a NOTE or WARNING (and submit the package as version 1.33.1)?
Thank You,
Charles
From: Alexey Sergushichev
Sent: Thursday, March 19, 2020 3:00 PM
To: Charles Warden
Cc: Shepherd, Lori ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
I think one of the major changes recently is setting stringsAsFactors
option to FALSE by default.
Best,
Alexey
On Fri, Mar 20, 2020 at 12:48 AM Charles Warden
mailto:cwar...@coh.org>> wrote:
Hi Lori,
Thank you very much.
If I use R-4.0 (instead of R-3.6), then I can reproduce the error message.
I will work in figuring out why the code works with R-3.6 but not R-4.0,
but it seems like this might affect other packages as well (since I received
error messages for 2 out of 2 of the Bioconductor packages that I contributed
to).
Do you have any general suggestions of what types of new errors might be
encountered from using R-4.0?
Thanks Again,
Charles
From: Shepherd, Lori
[mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>; Charles
Warden mailto:cwar...@coh.org>>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message
Yes that is the correct version of R to use. Thank you for taking the time
to make sure everything is correct to debug. We appreciate your effort and
contributors to bioconductor.
Get Outlook for
Android<https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$>
____
From: Charles Warden
mailto:cwar...@coh.org><mailto:cwar...@coh.org<mailto:cwar...@coh.org>>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori
mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>>;
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Lori,
Thank you very much for your response.
I was testing building the Bioconductor development branch, but I was using
R-3.6.
On the Ubuntu server where I have all the necessary dependencies
configured, I tested compiling R-devel but it didn't exactly say R-4.0.
So, in order to see if I can reproduce the error, I want to make sure I am
using the same version of R:
On the R website, it says "R version 4.0.0 (Arbor Day) prerelease
versions<https://urldefense.com/v3/__http:/cran.r
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Everybody, I think changing that read.table() parameter fixed the main issue. However, when I tested my code, R used a different way to note versions in R-v.4.0.0. For example, in order to clear a message from “R CMD check” or “R CMD build”, I had to say the version was 1.33-1 (instead of 1.33.1). I uploaded those changes to GitHub and tested an R-3.6 installation, and that was OK. However, when I am working on merging the GitHub and Bioconductor branches, I get the following error message: “Remote: Error: Illegal version bump from ‘1.33.0’ to ‘1.33-1’“ Is this going to be changed in Bioconductor, or should I see if this is only a NOTE or WARNING (and submit the package as version 1.33.1)? Thank You, Charles From: Alexey Sergushichev Sent: Thursday, March 19, 2020 3:00 PM To: Charles Warden Cc: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message I think one of the major changes recently is setting stringsAsFactors option to FALSE by default. Best, Alexey On Fri, Mar 20, 2020 at 12:48 AM Charles Warden mailto:cwar...@coh.org>> wrote: Hi Lori, Thank you very much. If I use R-4.0 (instead of R-3.6), then I can reproduce the error message. I will work in figuring out why the code works with R-3.6 but not R-4.0, but it seems like this might affect other packages as well (since I received error messages for 2 out of 2 of the Bioconductor packages that I contributed to). Do you have any general suggestions of what types of new errors might be encountered from using R-4.0? Thanks Again, Charles From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>] Sent: Thursday, March 19, 2020 1:41 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>; Charles Warden mailto:cwar...@coh.org>> Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message Yes that is the correct version of R to use. Thank you for taking the time to make sure everything is correct to debug. We appreciate your effort and contributors to bioconductor. Get Outlook for Android<https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$> ________ From: Charles Warden mailto:cwar...@coh.org><mailto:cwar...@coh.org<mailto:cwar...@coh.org>>> Sent: Thursday, March 19, 2020 4:37:52 PM To: Shepherd, Lori mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>> Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message Hi Lori, Thank you very much for your response. I was testing building the Bioconductor development branch, but I was using R-3.6. On the Ubuntu server where I have all the necessary dependencies configured, I tested compiling R-devel but it didn't exactly say R-4.0. So, in order to see if I can reproduce the error, I want to make sure I am using the same version of R: On the R website, it says "R version 4.0.0 (Arbor Day) prerelease versions<https://urldefense.com/v3/__http:/cran.r-project.org/src/base-prerelease__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVnoU6OsCs$> will appear starting Tuesday 2020-03-24. Final release is scheduled for Friday 2020-04-24.", but I can download prerelease files from the following page: https://cran.r-project.org/src/base-prerelease/<https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSaed1B9J$><https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$> I tested compiling the R-devel.tar.gz file. I think that completed without errors, but the version of R is reported as "R Under development (unstable) (2020-03-18 r78002)". So, I am not sure if this is correct. Is this the correct version of R to try and reproduce the error on my own computer? If not, can you please describe which file I should be using? I would like to install this separately from R 3.6 (in case the version of R affects other packages as well). Thank You, Charles From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>] Sent: Thursday, March 19, 2020 10:48 AM To: Charles Warden mailto:cwar...@coh.org><mailto:cwar...@coh.org<mailto:cwar...@coh.org>>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subje
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Alexey, Thank you very much – I will look into that. It does look like at least 1 demo dataset is being read incorrectly. Sincerely, Charles From: Alexey Sergushichev [mailto:alserg...@gmail.com] Sent: Thursday, March 19, 2020 3:00 PM To: Charles Warden Cc: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message I think one of the major changes recently is setting stringsAsFactors option to FALSE by default. Best, Alexey On Fri, Mar 20, 2020 at 12:48 AM Charles Warden mailto:cwar...@coh.org>> wrote: Hi Lori, Thank you very much. If I use R-4.0 (instead of R-3.6), then I can reproduce the error message. I will work in figuring out why the code works with R-3.6 but not R-4.0, but it seems like this might affect other packages as well (since I received error messages for 2 out of 2 of the Bioconductor packages that I contributed to). Do you have any general suggestions of what types of new errors might be encountered from using R-4.0? Thanks Again, Charles From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>] Sent: Thursday, March 19, 2020 1:41 PM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>; Charles Warden mailto:cwar...@coh.org>> Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message Yes that is the correct version of R to use. Thank you for taking the time to make sure everything is correct to debug. We appreciate your effort and contributors to bioconductor. Get Outlook for Android<https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$> ________ From: Charles Warden mailto:cwar...@coh.org><mailto:cwar...@coh.org<mailto:cwar...@coh.org>>> Sent: Thursday, March 19, 2020 4:37:52 PM To: Shepherd, Lori mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>> Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message Hi Lori, Thank you very much for your response. I was testing building the Bioconductor development branch, but I was using R-3.6. On the Ubuntu server where I have all the necessary dependencies configured, I tested compiling R-devel but it didn't exactly say R-4.0. So, in order to see if I can reproduce the error, I want to make sure I am using the same version of R: On the R website, it says "R version 4.0.0 (Arbor Day) prerelease versions<https://urldefense.com/v3/__http:/cran.r-project.org/src/base-prerelease__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVnoU6OsCs$> will appear starting Tuesday 2020-03-24. Final release is scheduled for Friday 2020-04-24.", but I can download prerelease files from the following page: https://cran.r-project.org/src/base-prerelease/<https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!-WIu-p4CrVw9hrXAGnmplvErU_cHTC8qgc8HQFuD1PD7ecyltJjSSaed1B9J$><https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$> I tested compiling the R-devel.tar.gz file. I think that completed without errors, but the version of R is reported as "R Under development (unstable) (2020-03-18 r78002)". So, I am not sure if this is correct. Is this the correct version of R to try and reproduce the error on my own computer? If not, can you please describe which file I should be using? I would like to install this separately from R 3.6 (in case the version of R affects other packages as well). Thank You, Charles From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>] Sent: Thursday, March 19, 2020 10:48 AM To: Charles Warden mailto:cwar...@coh.org><mailto:cwar...@coh.org<mailto:cwar...@coh.org>>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org><mailto:bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message It is not okay to ignore the emails you are getting. You need to investigate to find out if the ERROR is from your package or a package you depend on. While you have not made changes to the package, R has made a lot of changes to its base code that have broken a lot of packages. Most of the changes are being documented here http://bioconductor.org/developers/how-to/troubleshoot-build-report/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-re
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Lori,
Thank you very much.
If I use R-4.0 (instead of R-3.6), then I can reproduce the error message.
I will work in figuring out why the code works with R-3.6 but not R-4.0, but it
seems like this might affect other packages as well (since I received error
messages for 2 out of 2 of the Bioconductor packages that I contributed to).
Do you have any general suggestions of what types of new errors might be
encountered from using R-4.0?
Thanks Again,
Charles
From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 1:41 PM
To: bioc-devel@r-project.org; Charles Warden
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message
Yes that is the correct version of R to use. Thank you for taking the time to
make sure everything is correct to debug. We appreciate your effort and
contributors to bioconductor.
Get Outlook for
Android<https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$>
From: Charles Warden mailto:cwar...@coh.org>>
Sent: Thursday, March 19, 2020 4:37:52 PM
To: Shepherd, Lori
mailto:lori.sheph...@roswellpark.org>>;
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
mailto:bioc-devel@r-project.org>>
Subject: RE: Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Lori,
Thank you very much for your response.
I was testing building the Bioconductor development branch, but I was using
R-3.6.
On the Ubuntu server where I have all the necessary dependencies configured, I
tested compiling R-devel but it didn't exactly say R-4.0.
So, in order to see if I can reproduce the error, I want to make sure I am
using the same version of R:
On the R website, it says "R version 4.0.0 (Arbor Day) prerelease
versions<https://urldefense.com/v3/__http:/cran.r-project.org/src/base-prerelease__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVnoU6OsCs$>
will appear starting Tuesday 2020-03-24. Final release is scheduled for Friday
2020-04-24.", but I can download prerelease files from the following page:
https://cran.r-project.org/src/base-prerelease/<https://urldefense.com/v3/__https:/cran.r-project.org/src/base-prerelease/__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVng8C2GTW$>
I tested compiling the R-devel.tar.gz file. I think that completed without
errors, but the version of R is reported as "R Under development (unstable)
(2020-03-18 r78002)". So, I am not sure if this is correct.
Is this the correct version of R to try and reproduce the error on my own
computer? If not, can you please describe which file I should be using? I
would like to install this separately from R 3.6 (in case the version of R
affects other packages as well).
Thank You,
Charles
From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 10:48 AM
To: Charles Warden mailto:cwar...@coh.org>>;
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message
It is not okay to ignore the emails you are getting. You need to investigate
to find out if the ERROR is from your package or a package you depend on.
While you have not made changes to the package, R has made a lot of changes to
its base code that have broken a lot of packages. Most of the changes are
being documented here
http://bioconductor.org/developers/how-to/troubleshoot-build-report/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALMS8EdUs$>
Please remember that your github version of the repo is different than our
bioconductor git.bioconductor.org server.
http://bioconductor.org/developers/how-to/git/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALKJUJjjp$>
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALF7NFkcT$>
I can reproduce this locally on my computer. You will need to be using R 4.0
and Bioc 3.11 version of packages.
I ran R CMD Sweave COHCAP.Rnw to produce the R code in COHCAP.R
> library(COHCAP)
Loading required package: WriteXLS
Loading required package: COHCAPanno
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
> source("COHCAP.R", echo=TRUE)
> ### R code from vignette source
> '/home/lori/b/Rpacks/COHCAP/vignettes/COHCAP.Rnw'
>
> #
Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi Lori,
Thank you very much for your response.
I was testing building the Bioconductor development branch, but I was using
R-3.6.
On the Ubuntu server where I have all the necessary dependencies configured, I
tested compiling R-devel but it didn't exactly say R-4.0.
So, in order to see if I can reproduce the error, I want to make sure I am
using the same version of R:
On the R website, it says "R version 4.0.0 (Arbor Day) prerelease
versions<http://cran.r-project.org/src/base-prerelease> will appear starting
Tuesday 2020-03-24. Final release is scheduled for Friday 2020-04-24.", but I
can download prerelease files from the following page:
https://cran.r-project.org/src/base-prerelease/
I tested compiling the R-devel.tar.gz file. I think that completed without
errors, but the version of R is reported as "R Under development (unstable)
(2020-03-18 r78002)". So, I am not sure if this is correct.
Is this the correct version of R to try and reproduce the error on my own
computer? If not, can you please describe which file I should be using? I
would like to install this separately from R 3.6 (in case the version of R
affects other packages as well).
Thank You,
Charles
From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org]
Sent: Thursday, March 19, 2020 10:48 AM
To: Charles Warden ; bioc-devel@r-project.org
Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message
It is not okay to ignore the emails you are getting. You need to investigate
to find out if the ERROR is from your package or a package you depend on.
While you have not made changes to the package, R has made a lot of changes to
its base code that have broken a lot of packages. Most of the changes are
being documented here
http://bioconductor.org/developers/how-to/troubleshoot-build-report/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/troubleshoot-build-report/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALMS8EdUs$>
Please remember that your github version of the repo is different than our
bioconductor git.bioconductor.org server.
http://bioconductor.org/developers/how-to/git/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALKJUJjjp$>
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/<https://urldefense.com/v3/__http:/bioconductor.org/developers/how-to/git/sync-existing-repositories/__;!!Fou38LsQmgU!4jcx-leaLxfL2BEkbrsoQOxva2TZNrP3V15LcW-qR2EyDhkfpykALF7NFkcT$>
I can reproduce this locally on my computer. You will need to be using R 4.0
and Bioc 3.11 version of packages.
I ran R CMD Sweave COHCAP.Rnw to produce the R code in COHCAP.R
> library(COHCAP)
Loading required package: WriteXLS
Loading required package: COHCAPanno
Loading required package: RColorBrewer
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
> source("COHCAP.R", echo=TRUE)
> ### R code from vignette source
> '/home/lori/b/Rpacks/COHCAP/vignettes/COHCAP.Rnw'
>
> ###
> ### cod [TRUNCATED]
> dir = system.file("extdata", package="COHCAP")
> beta.file = file.path(dir,"GSE42308_truncated.txt")
> sample.file = file.path(dir,"sample_GSE42308.txt")
> expression.file = file.path(dir,"expression-Average_by_Island_truncated.txt")
> project.folder = getwd()
> project.name = "450k_avg_by_island_test"
> ###
> ### code chunk number 2: annotation
> ###
> be [TRUNCATED]
[1] 173 7
[1] 172 5
[1] 172 11
> ###
> ### code chunk number 3: site
> ###
> filtered [TRUNCATED]
[1] "Reading Sample Description File"
[1] 172 6
[1] 172 6
[1] "Differential Methylation Stats for 2 Groups with Reference"
[1] 172 5
[1] 172 10
[1] 172 10
[1] 34 10
[1] 34 10
> ###
> ### code chunk number 4: island
> ###
> island [TRUNCATED]
[1] "Reading Sample Description File"
[1] 172 6
[1] 172 6
[1] "Group: mutant" "Group: parental"
[1] "Checking CpG Site Stats Table"
[1] 34 10
[1] 29 10
[1] 5
[1] "Average CpG Sites per CpG Island"
[1] "Differential Methylation Stats for 2 Groups with Reference"
[1] 4 8
[1] 4 8
[1] "There are 4 differentially methylated islands"
[1] 4 8
[1] 4 8
[1] "Plotting Significant Islands Box-Plots.."
> ###
[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
Hi, I recently received error messages for 2 packages. As a worst-case-scenario, it is acceptable if the sRAP package had to be removed. However, I need to resolve the issue for the COHCAP package. This is odd because I don’t think I have updated either package in the last year or so. In fact, if I check the CHANGES file in the COHCAP package, the last change I manually noted was v1.29.3, which I can see was added to the GitHub version of the code on 3/2/2019: https://github.com/cwarden45/COHCAP/commits/master/CHANGES I can successfully install the package, with either the GitHub or Bioconductor instructions. However, I want to correct the error because I don’t want the Bioconductor package to be removed. I had some dependency issues on some systems related to the PDF generation (which I would usually ignore). However, if I run “R CMD build” on an Ubuntu system where I have all dependencies installed, I don’t get any error message: $ R CMD build COHCAP * checking for file ‘COHCAP/DESCRIPTION’ ... OK * preparing ‘COHCAP’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... OK Warning: ‘inst/doc’ files ‘COHCAP.Rnw’, ‘COHCAP.pdf’, ‘COHCAP.R’ ignored as vignettes have been rebuilt. Run R CMD build with --no-build-vignettes to prevent rebuilding. * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘COHCAP_1.33.0.tar.gz’ I am using the development version, which I thought should match what was being tested for the BioC 3.11 error message. Can you please either tell me what I need to do to reproduce (and then correct) this error, or confirm that it is OK to ignore the e-mails that I have received recently? Thank You, Charles Charles Warden, Bioinformatics Specialist Integrative Genomics Core City of Hope National Medical Center Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016) Room 1086 Internal Ext: 80375 | Direct: 626-218-0375 Work-From-Home Cell: 404-316-0012 -- -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] conditions on vectors of length > 1 Warning/ERROR
Hi Lori,
Thank you for pointing this out - I've added the any() function to the
function with the warning in the development version of COHCAP.
Thanks Again,
Charles
On Thu, Jan 25, 2018 at 9:44 AM, Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:
> Hello Bioconductor community,
>
> In a continued effort to better code, there have been efforts to identify
> problematic
> existing code in packages. The current issue at hand is identifying a
> conditional with a length greater than 1. This could either be an over site
> of not using any() or all() or could potential indicate problematic code
> with unexpected multiple output.
>
> dummy example:
>
> ```
> > check = c(1:5)
> > if (check > 3){
> +FALSE
> + }
> Warning message:
> In if (check > 3) { :
> the condition has length > 1 and only the first element will be used
> ```
>
> The following are packages that currently have code with this type of
> Warning/ERROR:
>
> cbaf
> COHCAP
> exomePeak
> ExtDist
> fabia
> gaia
> gCrisprTools
> GenVisR
> Guitar
> hapFabia
> KEGGlincs
> MassArray
> miRBaseVersions.db
> NOISeq
> pathview
> rHVDM
> SEPA
> sights
> support
> SVAPLSseq
>
>
> Please correct these issues as soon as possible. For a link to
> detailed output on what code is causing this, please see
>
> https://github.com/kalibera/rifcond
>
>
> We are implementing the check on incoming packages submitted to the
> Bioconductor tracker that will produce an ERROR and should be active by
> the end of next week.
>
> Thank you.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> This email message may contain legally privileged and/or confidential
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Re: [Bioc-devel] COHCAP GitHub Update
Hi Martin and Sean, Thanks for your help - I think the issue may be that I don't have a private key on the second computer (and the passcode still isn't recognized if I remove the .pub extension). I was trying to set up a deploy key on GitHub that would only apply to the COHCAP repository, but I will test having a public account key for the account (and do more testing before asking another question). Thanks, Charles On Sep 9, 2017 7:34 PM, "Martin Morgan" <martin.mor...@roswellpark.org> wrote: > On 09/09/2017 09:06 PM, Sean Davis wrote: > >> Hi, Charles. >> >> See inline. >> >> On Sat, Sep 9, 2017 at 8:40 PM, Charles Warden <cwarde...@gmail.com> >> wrote: >> >> Hi, >>> >>> I'm sorry, but I am having an issue setting up my ssh key. In >>> particular, >>> it is not recognizing the passcode (and I've tried copying over a new >>> id_rsa.pub file as well as double-checking the passcode): >>> >>> :~/.ssh$ ssh-add id_rsa.pub >>> Enter passphrase for id_rsa.pub: >>> Bad passphrase, try again for id_rsa.pub: >>> >>> >> Many folks do not use a passphrase (just hit enter when creating a new >> key) >> for ssh keys. It is potentially not as secure (in reality, probably not by >> much), but it does simplify things at least to start. >> >> >> >>> I also tried following these github instructions ( >>> https://help.github.com/ >>> articles/error-permission-denied-publickey/): I didn't see a solution, >>> but I can confirm the problem: >>> >>> ~/.ssh$ ssh -T g...@github.com >>> Permission denied (publickey) >>> >>> >> I'm not sure what the problem is at this point, but it seems pretty likely >> that figuring out what is broken and trying to fix it might be >> challenging. >> I would suggest starting over from scratch, using Github as a starting >> place. >> >> https://help.github.com/articles/connecting-to-github-with-ssh/ >> >> Once you get your key working with github from your various machines, then >> you can move ahead with the Bioconductor git server. >> >> - While it is tempting to make new ssh keys every time you need one, that >> has some very real disadvantages. Note that the github article has some >> notes about finding existing ssh keys. That said, in your case, a clean >> slate might be the easiest way to go, particularly since it appears that >> you might have misplaced the passphrase. >> - The file permissions on key files are important, so pay attention to >> notes about setting those correctly. >> >> >> >>> Since Sean was able to run "git clone g...@git.bioconductor.org:packa >>> ges/COHCAP.git", is there some other modification I should make to ssh >>> key? >>> >>> >> Git clone does not require permissions for public github repositories or >> for bioconductor package repositories. Only operations that involving >> "writing" to the git server require authentication, so the fact that I was >> able to clone your repo has nothing to do with my having correctly used an >> ssh key. Anyone, even without ANY ssh key, could have done so. >> > > actually, the Bioconductor git repository does not support reading using > ssh keys, only https. So any could do > > git clone https://git.bioconductor.org/packages/COHCAP > > but only people with valid ssh keys AND permissions can use > > git clone g...@git.bioconductor.org:packages/COHCAP > > (Sean -- you've got magical powers that carry over from svn days). > > I notice, Charles, that there are no keys registered with github > > https://github.com/cwarden45.keys > > I suggest that you figure things out using github, where you can see your > keys and where there is more public documentation. Also, note that you can > look at your local key pairs, for instance on Linux > > $ ls ~/.ssh/id* > /home/mtmorgan/.ssh/id_rsa /home/mtmorgan/.ssh/id_rsa.pub > > and I can confirm that the public part of the key pair > > $ cat ~/.ssh/id_rsa.pub > ssh-rsa B3NzaC1yc2EBIwAAAIEAwrnfSVn+lfnzSRwylWgC2Q7T0QJWvI8A > 0WHb8yMHF9OkgnldksS72OzjGr4qcz2kUsCb/ZsQTYj+g29zKUntbCSiLclEXBEz+lKUsdbG9z > awRiIypW60cfXKnbB3WfxkSqsiLDTtYDuaVAgS1htKwe6GV3aSYuMCge27ZlNhBWc= > mtmorgan@gopher4 > > matches the public part of the key pair registered on my github account. > (both github and Bioconductor support multiple key pairs). > > If you get to the point where your github public key is working, submit it > via the form using your svn id and github id. > >
Re: [Bioc-devel] COHCAP GitHub Update
Hi, I'm sorry, but I am having an issue setting up my ssh key. In particular, it is not recognizing the passcode (and I've tried copying over a new id_rsa.pub file as well as double-checking the passcode): :~/.ssh$ ssh-add id_rsa.pub Enter passphrase for id_rsa.pub: Bad passphrase, try again for id_rsa.pub: I also tried following these github instructions ( https://help.github.com/articles/error-permission-denied-publickey/): I didn't see a solution, but I can confirm the problem: ~/.ssh$ ssh -T g...@github.com Permission denied (publickey) Since Sean was able to run "git clone g...@git.bioconductor.org:packa ges/COHCAP.git", is there some other modification I should make to ssh key? If it matters, the original computer was a Mac OSX and the computer I am trying to manage COHCAP from is an Ubuntu VM (running within Windows). Also, the error message is the same if using the bioconductor git instead of the github: ~/.ssh$ ssh -T g...@git.bioconductor.org Permission denied (publickey). Thanks, Charles On Mon, Sep 4, 2017 at 5:28 PM, Sean Davis <seand...@gmail.com> wrote: > Hi, Charles. See replies inline. > > On Mon, Sep 4, 2017 at 3:30 PM, Charles Warden <cwarde...@gmail.com> > wrote: > >> Hi Sean, >> >> I'm admittedly on a different computer now, but I still get an error >> message (although it is different than the last one): >> >> git clone g...@git.bioconductor.org:packages/COHCAP.git >> Cloning into 'COHCAP'... >> Permission denied (publickey). >> fatal: Could not read from remote repository. >> >> Please make sure you have the correct access rights >> and the repository exists. >> > > This error means that there is a problem with your git ssh key. It could > be that your private key is not present on the new computer or that the ssh > key on Bioconductor has not been registered. Given the error below, it > appears that at least one ssh key is working. > > >> >> Also, there was a lot of text in the previous message, but I tried >> following the commands to merge and update the Bioconductor and GitHub >> COHCAP repositories. On that computer (the computer where I defined the >> ssh key), I could run "git remote add upstream g...@git.bioconductor.org: >> packages/COHCAP.git", but I ran into a problem at the push step: >> >> COHCAP cwarden$ git push upstream master >> >> To g...@git.bioconductor.org:packages/COHCAP.git >> >> ! [rejected]master -> master (non-fast-forward) >> >> error: failed to push some refs to 'g...@git.bioconductor.org: >> packages/COHCAP.git' >> >> hint: Updates were rejected because the tip of your current branch is >> behind >> >> hint: its remote counterpart. Integrate the remote changes (e.g. >> >> hint: 'git pull ...') before pushing again. >> > > You can often follow the instructions suggested by "hints" given by git. > In this case, it appears that there are some commits present at > Bioconductor that are not present in your local clone. Doing a `git pull` > will fetch and merge those changes. Assuming there are no merge conflicts, > you should then be able to push. > > >> >> >> hint: See the 'Note about fast-forwards' in 'git push --help' for details. >> >> Is there a way that I should modify the ssh "git clone >> g...@git.bioconductor.org:packages/COHCAP.git" command? >> > > You have had a few separate issues on this thread. My last comment about > `git pull` means that your first two problems (typo in the URL, missing or > mismatched ssh key) were overcome already. I'd proceed from there. > > Hope that helps, > Sean > > > >> >> Thanks, >> Charles >> >> On Mon, Sep 4, 2017 at 11:41 AM, Sean Davis <seand...@gmail.com> wrote: >> >>> Hi, Charles. >>> >>> The command is slightly off. Note the first '/' is a ':'. This worked >>> for me: >>> >>> git clone g...@git.bioconductor.org:packages/COHCAP.git >>> Cloning into 'COHCAP'... >>> remote: Counting objects: 485, done. >>> remote: Compressing objects: 100% (479/479), done. >>> remote: Total 485 (delta 329), reused 0 (delta 0) >>> Receiving objects: 100% (485/485), 104.78 KiB | 0 bytes/s, done. >>> Resolving deltas: 100% (329/329), done. >>> >>> Sean >>> >>> >>> On Mon, Sep 4, 2017 at 2:15 PM, Charles Warden <cwarde...@gmail.com> >>> wrote: >>> >>>> Hi Nitesh, >>>> >>>> Thanks. Unfortunately, I can't connect to the Bioconductor repository >>
Re: [Bioc-devel] COHCAP GitHub Update
in NAMESPACE Auto-merging DESCRIPTION CONFLICT (add/add): Merge conflict in DESCRIPTION Auto-merging CHANGES CONFLICT (add/add): Merge conflict in CHANGES [modified files to keep changes intended for SVN Bioconductor repository] COHCAP cwarden$ git add CHANGES COHCAP cwarden$ git add DESCRIPTION COHCAP cwarden$ git add NAMESPACE COHCAP cwarden$ git add man/COHCAP.BSSeq.preprocess.Rd COHCAP cwarden$ git add man/COHCAP.annotate.Rd COHCAP cwarden$ git add man/COHCAP.avg.by.island.Rd COHCAP cwarden$ git add man/COHCAP.avg.by.site.Rd COHCAP cwarden$ git add man/COHCAP.denovo.Rd COHCAP cwarden$ git add man/COHCAP.integrate.avg.by.island.Rd COHCAP cwarden$ git add man/COHCAP.integrate.avg.by.site.Rd COHCAP cwarden$ git add man/COHCAP.qc.Rd COHCAP cwarden$ git add man/COHCAP.site.Rd COHCAP cwarden$ git add man/COHCAP.reformatFinalReport.Rd COHCAP cwarden$ git add vignettes/COHCAP.Rnw COHCAP cwarden$ git add R/COHCAP.reformatFinalReport.R COHCAP cwarden$ git push upstream master To g...@git.bioconductor.org:packages/COHCAP.git ! [rejected]master -> master (non-fast-forward) error: failed to push some refs to 'g...@git.bioconductor.org: packages/COHCAP.git' hint: Updates were rejected because the tip of your current branch is behind hint: its remote counterpart. Integrate the remote changes (e.g. hint: 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details. Can you please help me troubleshoot updating the Bioconductor COHCAP repository via SSH? Thanks, Charles On Sun, Sep 3, 2017 at 7:07 PM, Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi > > You are using HTTPS protocol for cloning your repository. You need to use > SSH. > > > http://bioconductor.org/developers/how-to/git/new-package-workflow/ > > • SSH (developer) read / write access: g...@git.bioconductor.org > • HTTPS (public) read only access: https://git.bioconductor.org > > > Nitesh > > > On Sep 3, 2017, at 4:30 PM, Charles Warden <cwarde...@gmail.com> wrote: > > > > Hi Martin and Nitesh, > > > > Thanks for your help - I can now clone from the Bioconductor COHCAP git > repository, and I'm now working on syncing the GitHub repository and the > Bioconductor repository (or at least updating the Bioconductor repository). > > > > I'm testing making a minor change (not affecting functionality, in the > "CHANGES" text file) to one of the files from the Bioconductor repository > (without trying to sync the repositories), and I get the following error > message when I try to push the changes to the Bioconductor repository > (showing prior commands as well): > > > > cwarden$ git clone https://git.bioconductor.org/packages/COHCAP > > > > Cloning into 'COHCAP'... > > > > remote: Counting objects: 485, done. > > > > remote: Compressing objects: 100% (479/479), done. > > > > remote: Total 485 (delta 328), reused 0 (delta 0) > > > > Receiving objects: 100% (485/485), 107.97 KiB | 0 bytes/s, done. > > > > Resolving deltas: 100% (328/328), done. > > > > Checking connectivity... done. > > > > cwarden$ cd COHCAP > > > > COHCAP cwarden$ git checkout master > > > > Already on 'master' > > > > Your branch is up-to-date with 'origin/master'. > > > > [edit file] > > > > COHCAP cwarden$ git status > > > > On branch master > > > > Your branch is up-to-date with 'origin/master'. > > > > Changes not staged for commit: > > > > (use "git add ..." to update what will be committed) > > > > (use "git checkout -- ..." to discard changes in working > directory) > > > > > > > > modified: CHANGES > > > > > > > > no changes added to commit (use "git add" and/or "git commit -a") > > > > COHCAP cwarden$ git commit -a -m "fake commit" > > > > [master 225f7ac] fake commit > > > > 1 file changed, 1 insertion(+) > > > > COHCAP cwarden$ git status > > > > On branch master > > > > Your branch is ahead of 'origin/master' by 1 commit. > > > > (use "git push" to publish your local commits) > > > > > > nothing to commit, working directory clean > > > > COHCAP cwarden$ git push origin master > > > > fatal: remote error: FATAL: W any packages/COHCAP nobody DENIED by > fallthru > > > > (or you mis-spelled the reponame) > > > > > > I tried this on a couple computers and I get the same error message with > the "git push origin master" comman
Re: [Bioc-devel] COHCAP GitHub Update
Hi Martin and Nitesh, Thanks for your help - I can now clone from the Bioconductor COHCAP git repository, and I'm now working on syncing the GitHub repository and the Bioconductor repository (or at least updating the Bioconductor repository). I'm testing making a minor change (not affecting functionality, in the "CHANGES" text file) to one of the files from the Bioconductor repository (without trying to sync the repositories), and I get the following error message when I try to push the changes to the Bioconductor repository (showing prior commands as well): cwarden$ git clone https://git.bioconductor.org/packages/COHCAP Cloning into 'COHCAP'... remote: Counting objects: 485, done. remote: Compressing objects: 100% (479/479), done. remote: Total 485 (delta 328), reused 0 (delta 0) Receiving objects: 100% (485/485), 107.97 KiB | 0 bytes/s, done. Resolving deltas: 100% (328/328), done. Checking connectivity... done. cwarden$ cd COHCAP COHCAP cwarden$ git checkout master Already on 'master' Your branch is up-to-date with 'origin/master'. [edit file] COHCAP cwarden$ git status On branch master Your branch is up-to-date with 'origin/master'. Changes not staged for commit: (use "git add ..." to update what will be committed) (use "git checkout -- ..." to discard changes in working directory) modified: CHANGES no changes added to commit (use "git add" and/or "git commit -a") COHCAP cwarden$ git commit -a -m "fake commit" [master 225f7ac] fake commit 1 file changed, 1 insertion(+) COHCAP cwarden$ git status On branch master Your branch is ahead of 'origin/master' by 1 commit. (use "git push" to publish your local commits) nothing to commit, working directory clean COHCAP cwarden$ *git push origin master* *fatal: remote error: FATAL: W any packages/COHCAP nobody DENIED by fallthru* *(or you mis-spelled the reponame)* I tried this on a couple computers and I get the same error message with the "git push origin master" command. Can you please help me identify the problem, so I can at least update the Bioconductor repository? Thanks, Charles On Thu, Aug 24, 2017 at 11:07 AM, Charles Warden <cwarde...@gmail.com> wrote: > Hi Martin and Nitesh, > > Thanks for your help. > > I created a public ssh-key, I added it as a deploy key for the > Bioconductor package, and I provided that key in the git/svn transition > Google Doc file. > > I was trying to provide a key what would only affect the COHCAP package, > and not the other projects that are not Bioconductor projects. Please let > me know if this still works. > > Thanks, > Charles > > On Thu, Aug 24, 2017 at 5:59 AM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >> On 08/24/2017 07:27 AM, Turaga, Nitesh wrote: >> >>> http://bioconductor.org/developers/how-to/git/<http://biocon >>> ductor.org/developers/how-to/git/faq/>faq<http://bioconducto >>> r.org/developers/how-to/git/faq/>/<http://bioconductor.org/ >>> developers/how-to/git/faq/> >>> >>> Get Outlook for Android<https://aka.ms/ghei36> >>> >>> >>> From: Charles Warden <cwarde...@gmail.com> >>> Sent: Wednesday, August 23, 2017 11:32:42 PM >>> To: Turaga, Nitesh >>> Subject: Re: [Bioc-devel] COHCAP GitHub Update >>> >>> Hi Nitesh, >>> >>> I am getting a slightly different error message, now that I am changing >>> to be within the COHCAP directory: >>> >>> ## Start Code >>> >>> COHCAP cwarden$ git fetch --all >>> >>> Fetching origin >>> >>> Fetching upstream >>> >>> Permission denied (publickey). >>> >> >> this means that you do not have permissions to access your repository. >> This is probably because you, as an existing svn account holder, have not >> submitted an 'ssh' key to Bioconductor. >> >> The things you need to do are >> >> 1. create an ssh key pair, and submit the public key to your github >> account. Follow the link to 'add your public key to your GitHub account' in >> step 2 of >> >> http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ >> >> 2. submit your request for ssh access to git.bioconductor.org, >> following step 1 of >> >> http://bioconductor.org/developers/how-to/git/new-package-workflow/ >> >> (I will update the instructions at http://bioconductor.org/develo >> pers/how-to/git/maintain-github-bioc/ to include this step. >> >> 3. Wait 24 hours for manual processing >> >> 4. Try again &g
Re: [Bioc-devel] COHCAP GitHub Update
Hi Martin and Nitesh, Thanks for your help. I created a public ssh-key, I added it as a deploy key for the Bioconductor package, and I provided that key in the git/svn transition Google Doc file. I was trying to provide a key what would only affect the COHCAP package, and not the other projects that are not Bioconductor projects. Please let me know if this still works. Thanks, Charles On Thu, Aug 24, 2017 at 5:59 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 08/24/2017 07:27 AM, Turaga, Nitesh wrote: > >> http://bioconductor.org/developers/how-to/git/<http://biocon >> ductor.org/developers/how-to/git/faq/>faq<http://bioconduct >> or.org/developers/how-to/git/faq/>/<http://bioconductor. >> org/developers/how-to/git/faq/> >> >> Get Outlook for Android<https://aka.ms/ghei36> >> >> >> From: Charles Warden <cwarde...@gmail.com> >> Sent: Wednesday, August 23, 2017 11:32:42 PM >> To: Turaga, Nitesh >> Subject: Re: [Bioc-devel] COHCAP GitHub Update >> >> Hi Nitesh, >> >> I am getting a slightly different error message, now that I am changing >> to be within the COHCAP directory: >> >> ## Start Code >> >> COHCAP cwarden$ git fetch --all >> >> Fetching origin >> >> Fetching upstream >> >> Permission denied (publickey). >> > > this means that you do not have permissions to access your repository. > This is probably because you, as an existing svn account holder, have not > submitted an 'ssh' key to Bioconductor. > > The things you need to do are > > 1. create an ssh key pair, and submit the public key to your github > account. Follow the link to 'add your public key to your GitHub account' in > step 2 of > > http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ > > 2. submit your request for ssh access to git.bioconductor.org, > following step 1 of > > http://bioconductor.org/developers/how-to/git/new-package-workflow/ > > (I will update the instructions at http://bioconductor.org/develo > pers/how-to/git/maintain-github-bioc/ to include this step. > > 3. Wait 24 hours for manual processing > > 4. Try again > > some more below... > > > >> fatal: Could not read from remote repository. >> >> >> Please make sure you have the correct access rights >> >> and the repository exists. >> >> error: Could not fetch upstream >> >> ## End Code >> >> I also don't see COHCAP when I search the Bioconductor repository (when >> searching https://github.com/Bioconductor?utf8=%E2%9C%93=COHCAP; >> type==), and I also can't clone anything directory from >> Bioconductor: >> > > github.com/Bioconductor contains public versions of repositories > maintained by the Bioconductor core team; yours will not appear there. > > >> ## Start Code >> >> cwarden$ git clone g...@git.bioconductor.org:packages/COHCAP >> >> Cloning into 'COHCAP'... >> >> Permission denied (publickey). >> >> fatal: Could not read from remote repository. >> >> >> Please make sure you have the correct access rights >> >> and the repository exists. >> >> ## End Code >> >> I have my Bioconductor SVN username and password, but does something need >> to be initialized with the new git system (where I'll have a new >> Bioconductor username and password)? >> >> Thanks, >> Charles >> >> On Wed, Aug 23, 2017 at 2:18 PM, Turaga, Nitesh < >> nitesh.tur...@roswellpark.org<mailto:nitesh.tur...@roswellpark.org>> >> wrote: >> Hi >> >> On Aug 23, 2017, at 5:13 PM, Charles Warden <cwarde...@gmail.com>> cwarde...@gmail.com>> wrote: >>> >>> Hi, >>> >>> I downloaded code for the COHCAP Bioconductor SVN repository ( >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP/), >>> made >>> some changes, and then tried to commit those changes. However, I got an >>> error message that the SVN repository is locked, so the changes could not >>> be uploaded because of a switch to git. >>> >>> I have a GitHub account, and I uploaded the COHCAP code (with the latest >>> round of changes) to GitHub: >>> >>> https://github.com/cwarden45/COHCAP >>> >> >> So far so good. >> >>> >>> However, I am not sure how to make this the new Bioconductor >>
[Bioc-devel] COHCAP GitHub Update
Hi, I downloaded code for the COHCAP Bioconductor SVN repository ( https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP/), made some changes, and then tried to commit those changes. However, I got an error message that the SVN repository is locked, so the changes could not be uploaded because of a switch to git. I have a GitHub account, and I uploaded the COHCAP code (with the latest round of changes) to GitHub: https://github.com/cwarden45/COHCAP However, I am not sure how to make this the new Bioconductor repository. I am trying to follow the instructions available here: http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ However, if I run the command *git remote add upstream g...@git.bioconductor.org:packages/COHCAP.gi**t*, then I get an error message: *fatal: Not a git repository.* Can you please help me update the COHCAP Bioconductor repository and understand how this is now managed through GitHub? Also, I posted this question on the Support forum, but that may have not been the right venue. So, I apologize for the confusion. Thanks, Charles [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
